No abstract

Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research. Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples. Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites. Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries. Phylogenetic analyses indicated the existence of 12 independent clusters. Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters. We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research. Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan. Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.Genetic libraries of small subunit (SSU) ribosomal DNA (rDNA) genes constructed from environmental DNA have proven very valuable to study the taxonomic composition of marine prokaryotic plankton (8,16). Prokaryotic assemblages in the sea appeared to be dominated by novel bacterial and archaeal lineages (17), and this was an important breakthrough for understanding the structure and function of natural assemblages (37). Picoeukaryotes (eukaryotic microbes less than 2 to 3 m in diameter) are also recognized as fundamental components of marine ecosystems. Phototrophic picoeukaryotes contribute significantly to phytoplankton biomass and primary production (26), and heterotrophic picoeukaryotes, generally small flagellates (5), are the main grazers of bacteria and play key roles within the microbial food web (41). Despite the ecological importance of marine picoeukaryotes, the use of molecular tools to investigate their taxonomic composition, in particular by 18S rDNA libraries, is very recent (9, 28, 34). The most remarkable finding of these studies was the recovery of novel lineages within the stramenopile and alveolate phylogenetic divisions that accounted for a significant fraction of clones in the libraries. These novel lineages represent organisms that must contribute to marine processes but have not been investigated before and thus deserve further detailed phylogenetic and ecological studies.The stramenopiles (Heterokonta) form one of the eight major phylogenetic groups of eukaryo...

We analyzed picoeukaryote assemblages at a French coastal site of the English Channel by sequencing cloned eukaryotic 18S rRNA genes in eight genetic libraries constructed from environmental samples (seven coastal, one estuarine) collected at different periods of the year. Eight hundred clones were examined by amplified restriction fragment length polymorphism (RFLP) using the restriction enzyme HaeIII. The coverage value calculated from the relative distribution of RFLP types was low, indicating that the library diversity was not entirely recovered. A variable region of the rRNA gene was partially sequenced (550 bases) and analyzed for 397 clones. Thirty-two clones were affiliated with metazoans. Of the remaining clones, 132 were affiliated to algal classes (especially Prasinophyceae, Cryptophyceae, Dinophyceae, and Prymnesiophyceae) and 107 to known heterotrophic groups (Cercozoa, choanoflagellates, stramenopiles, and ciliates). One hundred three sequences fell into uncultivated groups of stramenopiles (43 clones) and alveolates (60 clones). We also found two potentially novel eukaryotic lineages, represented by 9 and 14 clones, respectively, not belonging to any known eukaryotic group. The overall composition of the picoeukaryote community remained fairly stable at the class/division level except during the early summer diatom bloom, when groups such as the Cryptophyceae and the ciliates completely disappeared. However, at a finer taxonomic level (corresponding to 98% sequence identity), the majority of the operational taxonomic units (OTU) were only observed once.